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Opened 23 months ago
Closed 23 months ago
#10324 closed defect (duplicate)
Unable to restore objects of NewerVersionQuery class
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.10.0-1050-oem-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202309300109 (2023-09-30 01:09:06 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Errors
---
errors | Bundle 'ChimeraX-Clipper' custom initialization failed
Bundle 'ChimeraX-ISOLDE' custom initialization failed
warnings | Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module
m = importlib.import_module(self.package_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/importlib/__init__.py", line
126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 940, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/home/dzyla/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/clipper/__init__.py", line 32, in <module>
__version__ = _version()
^^^^^^^^^^
File "/home/dzyla/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/clipper/__init__.py", line 30, in _version
return pkg_resources.require('ChimeraX-Clipper')[0].version
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 956, in require
needed = self.resolve(parse_requirements(requirements))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 815, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 861, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 10.1
(/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-Clipper'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 364, in initialize
api = self._get_api(session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api
m = self.get_module()
^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 492, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Clipper's module: (ChimeraX-AtomicLibrary 10.1 (/usr/lib/ucsf-chimerax-
daily/lib/python3.11/site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=12.0'), {'ChimeraX-Clipper'})
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module
m = importlib.import_module(self.package_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/importlib/__init__.py", line
126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 940, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/home/dzyla/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>
__version__ = _version()
^^^^^^^^^^
File "/home/dzyla/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 49, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 956, in require
needed = self.resolve(parse_requirements(requirements))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 815, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/pkg_resources/__init__.py", line 861, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ChimeraX-AtomicLibrary 10.1
(/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages),
Requirement.parse('ChimeraX-AtomicLibrary~=12.0'), {'ChimeraX-ISOLDE',
'ChimeraX-Clipper'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 364, in initialize
api = self._get_api(session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api
m = self.get_module()
^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 492, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: (ChimeraX-AtomicLibrary 10.1 (/usr/lib/ucsf-chimerax-
daily/lib/python3.11/site-packages), Requirement.parse('ChimeraX-
AtomicLibrary~=12.0'), {'ChimeraX-ISOLDE', 'ChimeraX-Clipper'})
> lighting soft
> camera ortho
> ui mousemode right "translate selected models"
> lighting soft
> hide atoms
> set bgColor #ffffff00
> camera ortho
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> lighting soft
UCSF ChimeraX version: 1.7.dev202309300109 (2023-09-30)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/dzyla/Phenix_media/HectoFab55/Hecto_Fab_2mer_combined-coot-5.pdb
Chain information for Hecto_Fab_2mer_combined-coot-5.pdb #1
---
Chain | Description
A | No description available
B E | No description available
C F | No description available
D | No description available
> lighting soft
> show cartoons
> hide atoms
> nucleotides tube/slab shape box
> interfaces ~solvent
6 buried areas: A D 1092, B C 817, E F 783, D E 662, A B 631, A C 363
> select clear
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> show cartoons
> hbonds (#1/A) restrict (/B-C) reveal true relax true distSlop 1.5 angleSlop
> 60
30 hydrogen bonds found
> style stick
Changed 9979 atom styles
> color byhetero
> color /B #7ee9ca
> color /C #7ed3e9
> color /C #456588
> color /B #7fa0a7
> color /B #1a303a
> color /B #5f8098
> color /B #1a303a
> color /C #5f8098
> color byhetero
> color /A #60507f
> color byhetero
> color /D #4a3c66
> color /D #372a4b
> lighting soft
> hide atoms
> set bgColor #ffffff00
> graphics silhouettes true width 5
> camera ortho
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> color /B gray
> color /B pink
> color /B magenta
> color /D #75639e
> color /B gray
> color /B #e3d3a3
> color /B #d9b3a2
> color /C #92716d
> color /C #c4cdc9
> color /D #715c87
> color /D #786976
> color /C #cca2a0
> color /B #db8368
> color /B #6f7f50
> color /C #dc9a22
> color /B #db8368
> color /B #8495af
> color /C #db8368
> color /C #8ebfd4
> color /C #cca2a0
> hbonds (#1/A) restrict (/B-C) reveal true relax true distSlop 1.5 angleSlop
> 60
30 hydrogen bonds found
> hide atoms
> hide #1.2 models
> color /C #7f4956
> color /B #bcb1aa
> style stick
Changed 9979 atom styles
> show atoms
> hbonds (#1/A) restrict (/B-C) reveal true relax true distSlop 1.5 angleSlop
> 60
30 hydrogen bonds found
> hide atoms
> hbonds (#1/A) restrict (/B-C) reveal true relax true distSlop 1.5 angleSlop
> 60
30 hydrogen bonds found
> show #1.2 models
> color byhetero
> save /home/dzyla/OneDrive/PostDOC/papers/HectoFab55/HectoFab55.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x7fa912476a90>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x7fa912476a90>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
> hide #1.2 models
> clip far -10
> clip far 10
[Repeated 10 time(s)]
> ui tool show "Side View"
> save /home/dzyla/OneDrive/PostDOC/papers/HectoFab55/Interface.png
> supersample 8 transparentBackground true height 2500
> hide atoms
> color /E #bcb1aa
> color /F #7f4956
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> save /home/dzyla/OneDrive/PostDOC/papers/HectoFab55/overview.png supersample
> 8 transparentBackground true height 2500
> save /home/dzyla/OneDrive/PostDOC/papers/HectoFab55/Hecto_fab55.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x7fa912476a90>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x7fa912476a90>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 545.23.08
OpenGL renderer: Quadro T2000 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 20TJS07400
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) W-10855M CPU @ 2.80GHz
Cache Size: 12288 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 23Gi 1.2Gi 1.1Gi 38Gi 37Gi
Swap: 2.0Gi 129Mi 1.9Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU117GLM [Quadro T2000 Mobile / Max-Q] [10de:1fb8] (rev a1)
Subsystem: Lenovo TU117GLM [Quadro T2000 Mobile / Max-Q] [17aa:22c0]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.4.0
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.7.22
cftime: 1.6.2
charset-normalizer: 3.3.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.11.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.48
ChimeraX-AtomicLibrary: 10.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.3
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.2
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.4
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202309300109
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7rc1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.1
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.12
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.11
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.1
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.10
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.32.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
contourpy: 1.1.1
cxservices: 1.2.2
cycler: 0.12.0
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.0
filelock: 3.9.0
fonttools: 4.43.0
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.2
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.0.5
wcwidth: 0.2.8
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 23 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Unable to restore objects of NewerVersionQuery class |
comment:2 by , 23 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Dawid,
--Eric